by Lisa Keilhofer

The mass extinction within

We all have come to face that we are amidst a gigantic mass extinction of global scope. The reasons for it are the rapid change that ecosystems are underlying, caused by climate change and utter destruction of habitats. In a nutshell, humans shape the planet faster than life on it is able to adjust to the new settings.

For a while now, we know that our body is – on its surface and also in the inside – home to billions of microorganisms. In thousands of years of co-existence, they have perfectly adjusted to the specific conditions they face and turned into useful and even more into essential tools. It is even more frightening to find that the mass extinction is not only affecting the world surrounding us, but also the ecosystem within us.

What is the state of our inner ecosystem?

The most densely populated area within us is our gut. The ratio of body-owned cells compared to microbial cells is 1:1,3. In that amount, our microbes add up to 1-3% of our total weight, which is some hundred grams (a detailed survey on who lives where can be found at 10 facts about the microbiome - MyMicrobiome). This is why many studies focus on the gut microbiome. And the findings are sobering: the variety of our intestinal ecosystem is dwindling.

We know this especially from comparative samples like one from Ötzi the stone age man, well-preserved bog-mummies, and other “donors” of that kind. Ötzi, to stick with the fist example, shows a significantly higher density and variety in gut colonization (1). A good reference for comparison is the bacterium Prevotella copri, which is especially needed for breaking down indigestive foods. The microbe helps reducing inflammation, and its ceasing prevalence is likely to encourage civilization diseases like diabetes, or irritable bowel syndrome. Its decline is often seen as indicator for the negative impact of modern life. Some tribes of indigenous people today, still have all four strains of P. copri, whereas the Western gut is home to but one strain. Ötzi’s gut, in comparison, featured also all four strains.

This decline in microbes is not just a few bacteria less, but a measurable impact to a highly complex and balanced ecosystem. A paper of Sandrine P. Claus underlines this, summarizing previous studies on P. copri in human gut and concludes that the problems are especially caused by the imbalance that the elimination of three in four strains brings with it (2).

Similar results were published in an article by the Institute of Mummy Research EURAC RESEARCH in Bolzano, Italy. Scientists were able to take samples from the stool remains of mummified corpses from the 7th century in a Mexican cave and analyzed the samples. The result: those bodies contained all four strains of P. copri, as well as the comparative groups from today’s Ghana and Tanzania (3).

To put this simple, one could say, the more strains of P. copri the more natural the way of life, the more intact the gut microbiome, the fewer the likeliness to suffer from civilization illnesses. At the same time, it is interesting that P. copri often cause inflammatory diseases. And once again, we see that in the world of bacteria, there is no “good” and “bad”. What is important, is the right bacterium in the right place in the right amount – a highly complex and fairly balanced system.

Where do we know that from?

The breakthrough in gut microbiome research was achieved by the latest technical developments. The crucial information about a microbe being pathogenic or naturally prevalent lies in their DNA, which needs high-throughput technology to be sequenced. A special publication by the science magazine “Spektrum” gives a good survey about the current research status (4).

Our way of life, nutrition, environment, medication and so on, influence the composition of our microbes. And as for every complex ecosystem on our planet goes: function and relevance of the individual microbe for the total system is still widely unknown. But we can tell by now that interfering with these complex systems mostly causes heavy damage.

How can we stop the mass extinction within us?

A lot is in a bad state, already, this is for sure. Changing our 21st century lifestyle back to a nature-bound living of indigenous people is simply not possible. Globalization and modern life have led to a way of life, we cannot just escape like that and the individual has only limited means to change that. Eating as little industrially processed food as possible, spending a lot of time outdoors, surround oneself with animals, steer clear of cosmetics, hygiene products, and detergents with antibacterial ingredients, and limit the intake of antibiotics to real emergencies – these are about the most important steps that every one of us can take immediately. And still, we are miles from the Ötzi way of life.

Most scientists believe it makes sense to preserve endangered microbes in an ark, until we are technically and medically able to re-colonize ourselves. One of these projects is “The Microbiota Vault” (5), in which scientists try to collect as many microbes from all around the world as possible and preserve them in a politically and geographically stable place. Laboratories in Norway or Switzerland are in the discussion for such potential places.

Also, “The American Gut Project” (6) or “The Earth Microbiome Project” (7) are examples for scientific approaches to capture and safe as much of the microbial diversity as possible. If there will be something like a standard-vaccine for every person or rather a probiotic treatment according to a specific deficiency remains to be seen. But what we know is that the mass extinction within us is in full progress and we need to take every step possible to give the following generations the chance to fall back on that diversity.

What are our chances?

The question for the chances of such projects is hard to answer. As all ecosystems, our gut turned out to be complex and very individual. The colonization of a fully functionable gut can and has to be quite different from case to case. A standard gavage of microbes therefore should be rather unrealistic, because even in the course of one single life, the composition of a healthy microbiome looks quite different at different times (8).

Reason for hope are for instance studies by Samuel Smits of the Stanford University (9). Smits and his team studied the microbiota in the guts of the Hadza in Tanzania and were able to prove that the composition varied greatly even within the course of one year. During the dry season, when the intake of foods is pretty diverse, the microbiome is much more diverse, too, compared to the rainy season. Some microbes that apparently are no longer needed in the wet season, decline as quickly that they are no longer verifiable in the guts. With the return of the dry season and the higher nutrition variety, however, they return year after year. This lets us hope that an intact microbiome can re-establish itself if only it gets the chance to.

Sources / References:

(1) Tett A, Huang K, The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations, Cell Host & Microbiome (2019),

(2) Claus S, The Strange Case of Prevotella copri: Dr. Jekyll or Mr. Hyde?, Cell Host & Microbiome (2019),

(3) Baumgartner B, Das Artensterben im Bauch, eurac research (2019),

(4) Viering K, Unsere Darmvielfalt ist bedroht, Spektrum (2019),


(6) McDonal D, Hyde E, American Gut: an Open Platform for Citizen Science Microbiome Research, Nation Lib of Med (2018),

(7) Gilbert J, Jansson J, Knight R, The Earth Microbiome project: successes and aspirations, BMC Biology (2014),,and%20adapt%20as%20new%20collaborators%20and...%20More%20

(8) Wilmanski T, Diener C, et al. Gut microbiome pattern reflects healthy ageing and predicts survival in humans. Nat Metab (2021).

(9) Smits S, Leach J,, Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania, Science (2017),

Lisa Keilhofer
Lisa Keilhofer

Lisa Keilhofer studied at the University of Regensburg. She works in internationalization and as a freelance editor.

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